RetrogeneDB ID: retro_pabe_12

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:111705828..111707217(+)
• Located in intron of: ENSPPYG00000016913

Retrocopy information

• Ensembl ID: ENSPPYG00000016914
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: EEF1A1
• Ensembl ID: ENSPPYG00000016777
• Aliases: EEF1A1, EEF1A
• Description: Elongation factor 1-alpha 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R4R8]

Sequence

>retro_pabe_12
ATGGGAAAGGAAAAGACTCATATCAACATTGTCGTCATTGGACACGTAGATTCGGGCAAGTCCACCACTACTGGCCATCT
GATCTATAAATGTGGTGGCATCGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCT
TCAAGTATGCCTGGGTCTTGGATAAACTGAAAGCTGAGCGTGAACGTGGTATCACCATTGATATCTCCTTGTGGAAATTT
GAGACCAGCAAGTACTATGTGACTATCATTGATGCCCCAGGACACAGAGACTTCATCAAAAACATGATTACAGGGACATC
TCAGGCTGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACCC
GAGAGCATGCCCTTCTGGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCA
CCCTACAGCCAGAAGAGATATGAGGAAATTGTTAAGGAAGTCAGCACTTACATTAAGAAAATTGGCTACAACCCCGACAC
AGTAGCATTTGTGCCAATTTCTGGTTGGAATGGTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGAT
GGAAAGTCACCCGTAAGGATGGCAATGCCAGTGGAACCACGCTGCTTGAGGCTCTGGACTGCATCCTACCACCAACTCGT
CCAACTGACAAGCCCTTGCGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGAATTGGTACTGTTCCTGTTGGCCGAGT
GGAGACTGGTGTTCTCAAACCCGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTACAACAGAAGTAAAATCTGTCGAAA
TGCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATGTT
CGTCGTGGCAACGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCT
GAACCATCCAGGCCAAATTAGCGCTGGCTATGCCCCTGTATTGGATTGCCACACGGCTCACATTGCATGCAAGTTTGCTG
AGCTGAAGGAAAAGATTGATCGCCGTTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGATGCTGCC
ATTGTTGATATGGTTCCTGGCAAGCCCATGTGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGCTTTGCTGTTCG
TGATATGAGACAGACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCTGGCAAGGTCACCAAGT
CTGCCCAGAAAGCTCAGAAGGCTAAATGA

Alignment

ORF - retro_pabe_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
          MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG
Retrocopy MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERG

Parental  ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
          ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA
Retrocopy ITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLA

Parental  YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW
          YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW
Retrocopy YTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPW

Parental  FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
          FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF
Retrocopy FKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTF

Parental  APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
          APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP
Retrocopy APVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHP

Parental  GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP
          GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP
Retrocopy GQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPP

Parental  LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
Retrocopy LGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.61 RPM	684.39 RPM
SRP007412_cerebellum	0.24 RPM	401.16 RPM
SRP007412_heart	1.38 RPM	800.63 RPM
SRP007412_kidney	3.94 RPM	2556.35 RPM
SRP007412_liver	1.53 RPM	1940.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

17 EST(s) were mapped to retro_pabe_12 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CR544911	111705899	111706476	99.9	576	1	575
CR545500	111706084	111706573	99.8	488	1	487
CR557655	111705928	111706623	99.8	691	2	688
CR629392	111705766	111706421	99.1	644	6	638
CR631105	111706012	111706503	99.8	490	1	489
CR753789	111705915	111706436	98.9	515	6	509
CR765090	111705893	111706569	99.8	671	2	668
CR765818	111705881	111706552	99.9	670	1	669
CR767093	111705928	111706583	99.9	652	1	651
CR767516	111705766	111706365	99	593	6	587
CR768286	111705882	111706507	99.2	619	5	613
CR768364	111705794	111706464	99.8	668	2	666
CR768921	111705766	111706502	99.2	727	6	721
CR787155	111705867	111706434	99.9	566	1	565
CR787666	111705938	111706639	99.5	696	4	692
CR788745	111705911	111706582	99.3	662	5	656
CR854383	111705766	111706418	99.3	647	5	642

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_12 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_12 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Echinops telfairi	ENSETEG00000004236	14 retrocopies	retro_etel_1189, retro_etel_1248, retro_etel_1260, retro_etel_1429, retro_etel_1436, retro_etel_1472, retro_etel_1578, retro_etel_1602, retro_etel_1682, retro_etel_1808, retro_etel_2135, retro_etel_366, retro_etel_411, retro_etel_830,
Gorilla gorilla	ENSGGOG00000025675	20 retrocopies	retro_ggor_1193, retro_ggor_1258, retro_ggor_1305, retro_ggor_1444, retro_ggor_1529, retro_ggor_20, retro_ggor_2006, retro_ggor_2021, retro_ggor_2056, retro_ggor_2066, retro_ggor_2205, retro_ggor_2526, retro_ggor_2637, retro_ggor_2826, retro_ggor_322, retro_ggor_375, retro_ggor_790, retro_ggor_860, retro_ggor_919, retro_ggor_978,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Microcebus murinus	ENSMICG00000015319	21 retrocopies	retro_mmur_1027, retro_mmur_1116, retro_mmur_1145, retro_mmur_1182, retro_mmur_1190, retro_mmur_12, retro_mmur_1282, retro_mmur_1316, retro_mmur_1339, retro_mmur_1343, retro_mmur_1350, retro_mmur_1568, retro_mmur_171, retro_mmur_26, retro_mmur_273, retro_mmur_49, retro_mmur_682, retro_mmur_729, retro_mmur_825, retro_mmur_877, retro_mmur_9,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Otolemur garnettii	ENSOGAG00000009152	10 retrocopies	retro_ogar_1215, retro_ogar_1622, retro_ogar_1779, retro_ogar_1840, retro_ogar_2281, retro_ogar_2526, retro_ogar_2557, retro_ogar_3013, retro_ogar_3046, retro_ogar_3271,
Pongo abelii	ENSPPYG00000016777	1 retrocopy	retro_pabe_12 ,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tupaia belangeri	ENSTBEG00000012151	51 retrocopies	retro_tbel_1084, retro_tbel_1330, retro_tbel_1373, retro_tbel_1452, retro_tbel_166, retro_tbel_1841, retro_tbel_1969, retro_tbel_1994, retro_tbel_2088, retro_tbel_2091, retro_tbel_2179, retro_tbel_2205, retro_tbel_2206, retro_tbel_2218, retro_tbel_2232, retro_tbel_2419, retro_tbel_2505, retro_tbel_259, retro_tbel_2627, retro_tbel_2718, retro_tbel_2738, retro_tbel_2758, retro_tbel_282, retro_tbel_2976, retro_tbel_3032, retro_tbel_3065, retro_tbel_3067, retro_tbel_3281, retro_tbel_3307, retro_tbel_3315, retro_tbel_338, retro_tbel_354, retro_tbel_360, retro_tbel_372, retro_tbel_3813, retro_tbel_3865, retro_tbel_3967, retro_tbel_4125, retro_tbel_4192, retro_tbel_4282, retro_tbel_4352, retro_tbel_4370, retro_tbel_4466, retro_tbel_4496, retro_tbel_4639, retro_tbel_4660, retro_tbel_4695, retro_tbel_473, retro_tbel_588, retro_tbel_620, retro_tbel_903,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,