RetrogeneDB ID: retro_ggor_2994

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:41458326..41459595(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TNIP2
• Ensembl ID: ENSGGOG00000025865
• Aliases: None
• Description: None

Sequence

>retro_ggor_2994
GACCCGGGGTCGGGAGGCCGGGAGGGGGCCCCGCGCGCAGCTGCAGAGCTCTGCGGCCTGTGCTACCAGGTCGGGTAGCG
GCTGCGGCGCCTGCAGGACCAGCTGGCCGCCCGCGACTCCCTCATCGCGTGCCTCCGCGCCAGGCTGGCCGCGCTGGAGG
GGTACACTGCGCCGTCCCTGGTGGACGCGCTGCTGGAGCAGGTGGCGCACTTCCGGGAGCAGCTGCAGCGGCAGGAGAAC
GGCGCCGCGGAGGCCCAGATGCGCCAGGAAATTGAGAGGCTTACTGAACGACTAGAAGCGAAAGAGAGGGAGATGCAGCA
GCTGCTGAGCCAGCCACAGCACGAGCGAGAGAAGGAAGTCGTCCTGATGCGGAGGAGCATGGCGGAGGGCGAACTGGCCC
ACCCCGCCAGTGACGTTCTGTGCAGCTCCTTGGCCAATGAGACCCACCAGCTGCGGAGGACGCTGACCTCCACTGCCCAC
ATGTGTCAGCATCTGGCCAAGTGTCTGGATGAACGACAGCATGCACAAAGGAACGTGGGGGAGAGAAGTCCTGAAAGTCA
GAACATACAGGTAGGGACACCTCTGTCCAGAGTGTTACTGAGGAAGAAAATGAACTGTTAAAACAGAACGTGACTCACGT
TGAAGACCTCAATGCCAAGTGGCAGCTATACGATGCCAGCAGGGACGAATACATGAGGGGGCTCCATGCACAGCTCAGGG
GGCTGCAGACCCCCCATGAGCCCGAGCTGATGAGGAAAGAGATCTCCCGGCTCAACAGATAGTTGGAAGAGAAAATAAAC
GACTGTGCAGAATTGAAGTAGAAGCTGGCAGCCTCGAGGACGGCACGGGATGCTGCACTGGAATGGGTGCAGATACTGGA
ATAGCAGATTCTCGCGTACAAGGATGACTTCATGTCAGAAAGGGCAGATCGGGAACAGGCTCAAGGTAGGATTCAGGAAC
TGGAGGAAAAGGTCACCTCTTTGCTGCACCAGGTGTCCTGGAGACAGGATTCTCAAGAGCCAGACGCCGGCTGGATTCAC
GCTGGGAGCAAAACTGCCAAGTACTTGGCCACCGATGCAGTGGAGCTTATGGTGCCTGGTGGCTGGAGGCCTGGGACTGG
GTCCCAGGCAGTTGGAACCCCCTGCAGAGGGCGGGCATCCTGGCGCAGCCCAGAGAGGCCAGGGGGACCTTCAGTGCCCT
CACTGCCTGCAGTGCTTCAGTGATGAACAAGGTGAAGAGCTCCTCAGGCACGTGGCTGAGTGCTGCCAG

Alignment

ORF - retro_ggor_2994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.62 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DPGSGGWEGAPRAAAALCTLYHEAGQRLRRLQDQLAARDALIARLRARLAALEGDAAPSLVDALLEQVAR
          DPGSGG.EGAPRAAA.LC.L....G.RLRRLQDQLAARD.LIA.LRARLAALEG..APSLVDALLEQVA.
Retrocopy DPGSGGREGAPRAAAELCGLCYQVG*RLRRLQDQLAARDSLIACLRARLAALEGYTAPSLVDALLEQVAH

Parental  FREQLRRQEGGAAEAQMRQEIERLTERLEEKEREMQQLLSQPQHEREKEVVLLRRSMAEGERARAASDVL
          FREQL.RQE.GAAEAQMRQEIERLTERLE.KEREMQQLLSQPQHEREKEVVL.RRSMAEGE.A..ASDVL
Retrocopy FREQLQRQENGAAEAQMRQEIERLTERLEAKEREMQQLLSQPQHEREKEVVLMRRSMAEGELAHPASDVL

Parental  CRSLANETHQLRRTLTATAHMCQHLAKCLDERQHAERNVGERSPD-QSEHTDGHTSVQSVIEKLQEENRL
          C.SLANETHQLRRTLT.TAHMCQHLAKCLDERQHA.RNVGERSP...SEHT...TSVQSV.E...EEN.L
Retrocopy CSSLANETHQLRRTLTSTAHMCQHLAKCLDERQHAQRNVGERSPE<KSEHTGRDTSVQSVTE---EENEL

Parental  LKQKVTHVEDLNAKWQRYDASRDEYVRGLHAQLRGLQIPHEPELMRKEISRLNRQLEEKINDCAEVKQEL
          LKQ.VTHVEDLNAKWQ.YDASRDEY.RGLHAQLRGLQ.PHEPELMRKEISRLNR.LEEKINDCAE.K..L
Retrocopy LKQNVTHVEDLNAKWQLYDASRDEYMRGLHAQLRGLQTPHEPELMRKEISRLNR*LEEKINDCAELK*KL

Parental  AASRTARDAALERVQMLEQQILAYKDDFMSERADRERAQSRIQELEEKVASLLHQVSWRQDSREPDAGRI
          AASRTARDAALE.VQ.LE.QILAYKDDFMSERADRE.AQ.RIQELEEKV.SLLHQVSWRQDS.EPDAG.I
Retrocopy AASRTARDAALEWVQILE*QILAYKDDFMSERADREQAQGRIQELEEKVTSLLHQVSWRQDSQEPDAGWI

Parental  HAVSKTAKYLATDALELMVPGGWRPGTGSQ-QLEPPAEGGHPGAAQRGQGDLQCPHCLQCFSDEQGEELL
          HA.SKTAKYLATDA.ELMVPGGWRPGTGSQ.QLEPPAEGGHPGAAQRGQGDLQCPHCLQCFSDEQGEELL
Retrocopy HAGSKTAKYLATDAVELMVPGGWRPGTGSQ>QLEPPAEGGHPGAAQRGQGDLQCPHCLQCFSDEQGEELL

Parental  RHVAECCQ
          RHVAECCQ
Retrocopy RHVAECCQ

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	0.00 RPM	7.19 RPM
SRP007412_cerebellum	0.00 RPM	3.47 RPM
SRP007412_heart	0.00 RPM	8.79 RPM
SRP007412_kidney	0.00 RPM	19.05 RPM
SRP007412_liver	0.00 RPM	13.85 RPM
SRP007412_testis	0.10 RPM	9.84 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_2994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2994 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4809
Pongo abelii	retro_pabe_3737

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000168884	1 retrocopy	retro_hsap_4809,
Gorilla gorilla	ENSGGOG00000025865	1 retrocopy	retro_ggor_2994 ,
Nomascus leucogenys	ENSNLEG00000000191	1 retrocopy	retro_nleu_2184,
Pongo abelii	ENSPPYG00000014545	1 retrocopy	retro_pabe_3737,