RetrogeneDB ID: retro_pabe_1516

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:57880193..57880967(-)
• Located in intron of: ENSPPYG00000008570

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSPPYG00000009405
• Aliases: None
• Description: SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]

Sequence

>retro_pabe_1516
AACTTTAGTGACACACTGCTGGATGCCGGCGAGTCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAAGT
CAAGTAGAACTTCATTGATCTCCTCCAGAACCTGTGTGAGAAAGACCTGAAGGGGATCCCACACCACCTGCAGAAGCTGG
AGGGCCGCCGCCTGGACTTAGACTAAAAGAAGCAGCAGGGCAAGATCCCCAATGAGGAGCTACACCAGGCGCTGGAGAAG
TTTGAGGACTCCAAGGAGGTAGAAGAAATCAGCATGCACAACCACCTGGAGACCAACATTGAGCAGGTGAGTCAACTCTG
GGCCCTGGTGGAGGCGCAGCTGGACTACCACTGGCAGGCCATGCAGATCCTGGACGAGCTGGCAGAGAAGCTCAAGCGCA
GGATGCGGGAAGCTTCCTCACGCCCCAAGAGGGAGTATAAGCCCAAGTCCCGGGAGCCCTTTGACCTCGGAGAGCCTGAG
CAGTCCAACGGGGGCTTCCCCTGCACCACACTCCCCAAGATTGCAGCTTCATTCTCTTTCCCATCTTCCGACAAGCCCAT
CCGGACTCCTAGCAGGAGCATGCCGCCCCTAGAACAGCCAAGCTGCAAGGTGCTGTACGACTTCCAGCCTGAGAACGATG
GGGAGCTGGGCTTCCATGAAGGCGATGTCTTCACGCTGATCAACCAGATCAACGAGAAGTGGTACCAGGGCATGCTGGAC
GGCCAGTTGGGCTTCTTCCTGCTCAGCTACTTGGATGTGCTTGTGCCTCTGCCC

Alignment

ORF - retro_pabe_1516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.17 %
• Parental protein coverage: 84.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NPGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKI
          N..D.LLDAGESMK.LAEVKDSLDIEVK.NFID.LQNLCEKDLK.I.HHL.KLEGRRLD.D.KK..QGKI
Retrocopy NFSDTLLDAGESMKHLAEVKDSLDIEVK*NFIDLLQNLCEKDLKGIPHHLQKLEGRRLDLD*KKQ-QGKI

Parental  PDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMREAS
          P.EEL.QALEKFE.SKEV.E.SMHN.LET.IEQVSQL.ALV.AQLDYH.QA.QILDELAEKLKRRMREAS
Retrocopy PNEELHQALEKFEDSKEVEEISMHNHLETNIEQVSQLWALVEAQLDYHWQAMQILDELAEKLKRRMREAS

Parental  SRPKREYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALYDFE
          SRPKREYKPK.REPFDLGEPEQSNGGFPCTT.PKIAAS.SF.SSDKPIRTPSRSMPPL.QPSCK.LYDF.
Retrocopy SRPKREYKPKSREPFDLGEPEQSNGGFPCTTLPKIAASFSFPSSDKPIRTPSRSMPPLEQPSCKVLYDFQ

Parental  PENDGELGFREGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVPLP
          PENDGELGF.EGDV.TL.NQI.E.WY.GMLDGQ.GFF.LSY..VLVPLP
Retrocopy PENDGELGFHEGDVFTLINQINEKWYQGMLDGQLGFFLLSYLDVLVPLP

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	1.16 RPM	28.53 RPM
SRP007412_cerebellum	2.68 RPM	17.15 RPM
SRP007412_heart	0.57 RPM	5.06 RPM
SRP007412_kidney	1.76 RPM	29.07 RPM
SRP007412_liver	0.64 RPM	21.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1516 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1516 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1516 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1859
Gorilla gorilla	retro_ggor_2151

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745, retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516 , retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,