RetrogeneDB ID: retro_ggor_2066

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:145005152..145006537(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000022861
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_2066
ATGGGAAAGGAAAAAACTCATATCAACATTGTCGTCATTGGACATGTAGATTCAGGCAGGTCCACCACTACTGGCCATCT
GATCTACAAATGTAGTGGCATCGACAAAAGAACCATTGAAAAATTTGAGAAGGAGGCTGGCTGAGATGGGAAAGGGCTCC
TTCAAGTATGCCTGGGTCTTGGGTAAACTGAAAGCTGAGTGTGAACGTGGTATCACCATTGATATCTCCTTGTAGAAATT
TGAGACCAGCAGGTACTACATGGCTATCATTGATACCCCAGGACACAGAGACTTCATCAAAAACCTGATTACAGGGATAT
CTCAGGCTGACTGTAACGTCCTAAATGTTGCTGCTGGTGTTGGTGAATTTGAAGCTGGGAACTTCAAAAATGGGCAGACC
CGAGAGCATGCCCTTCTGGTTTACACACTGGGTGTGAACAACTAATCATTTGTGTTAACAAAATGGATTCCACTGAGCCA
CCTTACAGCCAGAAGAGATATCAGGGAATCGTTAAGGAAGTCAGCACTTACATTAAGAAATCGGCTACAACCCTGACACA
GTAGCGTTTGTGCCAATTTCTGGTTGGAATGTTGACAACATGCTGGAGCCAAGTGCTAACATGCCTTGGTTCAAGGGATG
GAAAGTCACCTGTAAGGATGGCAATACCAGTGGAACCACGCTGCTTGAGGCTCTGGACTGCATCCTATCACTGATTTGTC
CAACTGACAAGCCCACGTGCCTGACTCTTCAGGATGTCTACAAAATTGGTGGTATTGGTGCTGTTCCTGTAGGTCGAGTG
GAGACTGATGTTTTCAAACCTACTATGGTGGCCACCTTTGCTCCAGTCAACAATACAACTGAAGTAAAATCTGTCGAAAT
GCACCATGAAGCTTTGAGTGAAGCTCTTCCTGGGGACAATGTGGGCTTCAATGTCAAGAATGTGTCTGTCAAGGAGGTTC
ATCATGGCGATGTTGCTGGTGACAGCAAAAATGACCCACCAATGGAAGCAGCTGACTTCACTGCTCAAGTGATTATCCTG
AACCATTCAGGCCAAATCAGCGCTGGCTATGCCTCTGTACTGGATTGCCACATGGCTCACATTGCATGCCAGTTTGCTGA
GCTGAAGGAAAAGATTGATTGCCGTTCTGGTAAAAAGCTGGAAGATGGTCCTAAATTCTTGAAGTCTGGTGATGCTGCCA
TCATTGATATGGTTCCTGGCAAGCCTATGTGTGTTGAGAGCTTCTCAGACTATCCACCTCTGCATCGCTTTGCTGTTCAT
GATATGAGACAGACAGTTGTCCTGGGTGTCATCAAAGCAGTGGACAAGAAGGCTGCTGGAGCAGGCAAGGCCACTAAGTC
TGCTCAGAAAGCTTAGAAGGCCAAA

Alignment

ORF - retro_ggor_2066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MGKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEA-AEMGKGSFKYAWVLDKLKAERER
          MGKEKTHINIVVIGHVDSG.STTTGHLIYKC.GIDKRTIEKFEKEA.AEMGKGSFKYAWVL.KLKAE.ER
Retrocopy MGKEKTHINIVVIGHVDSGRSTTTGHLIYKCSGIDKRTIEKFEKEA>AEMGKGSFKYAWVLGKLKAECER

Parental  GITIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTREHALL
          GITIDISL.KFETS.YY..IID.PGHRDFIKN.ITG.SQADC.VL.VAAGVGEFEAG..KNGQTREHALL
Retrocopy GITIDISL*KFETSRYYMAIIDTPGHRDFIKNLITGISQADCNVLNVAAGVGEFEAGNFKNGQTREHALL

Parental  AYTLGV-KQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKK-IGYNPDTVAFVPISGWNGDNMLEPSAN
          .YTLGV..QLI..VNKMDSTEPPYSQKRY..IVKEVSTYIKK.IGYNPDTVAFVPISGWN.DNMLEPSAN
Retrocopy VYTLGV<EQLIICVNKMDSTEPPYSQKRYQGIVKEVSTYIKK<IGYNPDTVAFVPISGWNVDNMLEPSAN

Parental  MPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVLKPGMV
          MPWFKGWKVT.KDGN.SGTTLLEALDCIL....PTDKP..L.LQDVYKIGGIG.VPVGRVET.V.KP.MV
Retrocopy MPWFKGWKVTCKDGNTSGTTLLEALDCILSLICPTDKPTCLTLQDVYKIGGIGAVPVGRVETDVFKPTMV

Parental  VTFAPVNVTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFTAQVIIL
          .TFAPVN.TTEVKSVEMHHEALSEALPGDNVGFNVKNVSVK.V..G.VAGDSKNDPPMEAA.FTAQVIIL
Retrocopy ATFAPVNNTTEVKSVEMHHEALSEALPGDNVGFNVKNVSVKEVHHGDVAGDSKNDPPMEAADFTAQVIIL

Parental  NHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVESFSD
          NH.GQISAGYA.VLDCH.AHIAC.FAELKEKID.RSGKKLEDGPKFLKSGDAAI.DMVPGKPMCVESFSD
Retrocopy NHSGQISAGYASVLDCHMAHIACQFAELKEKIDCRSGKKLEDGPKFLKSGDAAIIDMVPGKPMCVESFSD

Parental  YPPLGRFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
          YPPL.RFAV.DMRQTV..GVIKAVDKKAAGAGK.TKSAQKA.KAK
Retrocopy YPPLHRFAVHDMRQTVVLGVIKAVDKKAAGAGKATKSAQKA*KAK

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	0.29 RPM	813.64 RPM
SRP007412_cerebellum	0.04 RPM	767.71 RPM
SRP007412_heart	0.06 RPM	312.04 RPM
SRP007412_kidney	0.41 RPM	4298.85 RPM
SRP007412_liver	0.32 RPM	2725.93 RPM
SRP007412_testis	0.21 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_2066 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2066 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2983
Macaca mulatta	retro_mmul_1906

---

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,