RetrogeneDB ID: retro_ggor_2056

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:114818555..114819935(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGGOG00000025675
• Aliases: None
• Description: Elongation factor 1-alpha [Source:UniProtKB/TrEMBL;Acc:G3S518]

Sequence

>retro_ggor_2056
AAGGAAAAGACTCATATCAACACTGTGATCATCGGGCACGTAGAGTCGGGCAAGTCCACCACTACTGGCCATCTGATCTA
CAAACGCGGTGGCGTCGACAAAAGAACCATCGAAAAATTTGAGAAGGAGGCTGCTGAGATGGGAAAGGGCTCCTTCAAGT
ACGCCTGGGTCTTGGATAAACTGAAAGCTGAGCGTGAACGTGGTATCACCATTGATATCTCCTTGTGGAAATTTGAGACC
AGCAAGTACTATGTGACTATCCTTGATGCCCCAGGACACAGAGACCTCATCAAAAACGTGATTACAGGGACACCTCAGGC
TGACTGTGCTGTCCTGATTGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGTATCTCCAAGAATGGGCAGACCCGAGAGC
ATGCCCTTCTAGCTTACACACTGGGTGTGAAACAACTAATTGTTGGTGTTAACAAAATGGATTCCACTGAGCCACCCTAC
AGCCATAAGAGATATGAGGAAATTGTTAAGGAAGTCAGCACTTACATTAAGAAAATTGGCTACAACACCGACACAGTAGC
ATTTGTGCCAGTTTCTGGTTGGAATGGTGACAACACGCTGGAGCCAAGTGCTAACATGCCTTGATTCAAGGGATAGAAAG
TCACCCATAAGGATGGCAATGCCAGTGGAACCACGCTGCTTGAGGCTCTTGACTGCATCCTACCACCAACTCGTCCAACT
GACAAGCCCTTGTGCCTGCCTCTCCAGGATGTCTACAAAATTGGTGGTATTGGTACTGTTCCTGTTGGCTGAGTGGAGAC
TGGTGTTCTCAAACCTGGTATGGTGGTCACCTTTGCTCCAGTCAACGTTGCAACAGAAGTAAAATCTGTCGAAATGCACC
ATGAAGCTTTGAGTGAAGCTCTTCCTGGGAACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGATGTTCGTCGT
GGCAACGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGGCTTCACTGCTCAGGTGATTATCCTGAACCA
TCCAGGCCAAATAAGTGCTGGCTATGCCCCTGTATTGGATTGCCACACGGCTCACATTGCATGCAAGTTTGCTGAGCTGA
AGGAAAAGACTGATCACCATTCTGGTAAAAAGCTGGAAGATGGCCCTAAATTCTTGAAGTCTGGTGAAGCTGCCATTGTT
GATATGGTTCCTGGCAAGCCCGTGTGTGTTGAGAGCTTCTCAGACTATCCACCTTTGGGTCGCTTTGCTGTTCATGATAT
CAGACAGACAGTTGCGGTGGGTGTCATCAAAGCAGTGGACAAGAACGCTGCTGGAGCTGGCAAGGTCACCAAGTCTGCCC
AGAAAGCTCAGAAGGCTAAA

Alignment

ORF - retro_ggor_2056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGIT
          KEKTHIN.V.IGHV.SGKSTTTGHLIYK.GG.DKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGIT
Retrocopy KEKTHINTVIIGHVESGKSTTTGHLIYKRGGVDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGIT

Parental  IDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYT
          IDISLWKFETSKYYVTI.DAPGHRD.IKN.ITGT.QADCAVLIVAAGVGEFEAGISKNGQTREHALLAYT
Retrocopy IDISLWKFETSKYYVTILDAPGHRDLIKNVITGTPQADCAVLIVAAGVGEFEAGISKNGQTREHALLAYT

Parental  LGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMPWFK
          LGVKQLIVGVNKMDSTEPPYS.KRYEEIVKEVSTYIKKIGYN.DTVAFVP.SGWNGDN.LEPSANMP.FK
Retrocopy LGVKQLIVGVNKMDSTEPPYSHKRYEEIVKEVSTYIKKIGYNTDTVAFVPVSGWNGDNTLEPSANMP*FK

Parental  GWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMVVTFAP
          G.KVT.KDGNASGTTLLEALDCILPPTRPTDKPL.LPLQDVYKIGGIGTVPVG.VETGVLKPGMVVTFAP
Retrocopy G*KVTHKDGNASGTTLLEALDCILPPTRPTDKPLCLPLQDVYKIGGIGTVPVG*VETGVLKPGMVVTFAP

Parental  VNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQ
          VNV.TEVKSVEMHHEALSEALPG.NVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQ
Retrocopy VNVATEVKSVEMHHEALSEALPGNNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIILNHPGQ

Parental  ISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSDYPPLG
          ISAGYAPVLDCHTAHIACKFAELKEK.D..SGKKLEDGPKFLKSG.AAIVDMVPGKP.CVESFSDYPPLG
Retrocopy ISAGYAPVLDCHTAHIACKFAELKEKTDHHSGKKLEDGPKFLKSGEAAIVDMVPGKPVCVESFSDYPPLG

Parental  RFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          RFAV.D.RQTVAVGVIKAVDK.AAGAGKVTKSAQKAQKAK
Retrocopy RFAVHDIRQTVAVGVIKAVDKNAAGAGKVTKSAQKAQKAK

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	0.67 RPM	813.64 RPM
SRP007412_cerebellum	0.63 RPM	767.71 RPM
SRP007412_heart	0.22 RPM	312.04 RPM
SRP007412_kidney	2.58 RPM	4298.85 RPM
SRP007412_liver	1.56 RPM	2725.93 RPM
SRP007412_testis	1.04 RPM	1470.18 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2056 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 87 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,
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,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,