RetrogeneDB ID: retro_ttru_1151

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_105762:113271..114540(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSTTRG00000009022
• Aliases: None
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]

Sequence

>retro_ttru_1151
AAATTTGGTGAGTGGCTTCCACCTAAATGATTTACTAGGGAAGCTATGTGAAGTTATTTAAAAGAGCAAGGGGATCAAAC
AGTACTACTTATTCTTCATGCAAAAGTTGCACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTTGCCCTCCTCCTTGTG
TGTATCTTATGGGCAGTGGATGGAAGGAAAAAAAGAACAAATGGAACGCGATGGTTGTTCTGAACAAGAGTCTCAACCCT
GTGCATTTATTAGAATAGGAAATAGTGACCAAGAAATGCAGCAGCTAAACTGGGAAGGAAAGAACTATTGCACGGCCAAA
ACATTGTATATATCCGACTCAGACAAGAGAAAGCACTTCATGCTCTCTGTGAAGATGTTCTATGGCAGTAGTGATGACAT
TGGTGTGTTCCTCAGCAAACAGATAAAAGTCACCTCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGACTTAT
GCATTGCCTCAGGAACAAAGGTGGCTCTGTTTAATCGACTTCGATCCCAGACAGTTAGTACCAGATGCTTGCATGTAGAA
GGAGGTAATTTCCATGCCAGTTCTCAGCAGTGGGCAGCATTTTACATTCATCTCTTGGATGATGATGAATCAGAAGGAGA
AGAATTCACAGTCCACGATGGATACATCCATTATGGACAAACAGTCACACTTGTGTGTTCAGTTACTGGCGTGGCACTCC
CAAGGTTGATAATTAGGAAAGTTGATAAGCAAACCGCATTACTGGACGCAGGTGATCCTGTGTCACAGCTCCATAAATGT
GCATTTTACCTTAAGGATACAGAAAGAATGTACTGTGCCTTTCTCAAGAAAGAATAGTTCGGTTTCAGGCCACTCCATGC
CCAAAAGAACCAAATAAAGAGATGATAAATGATGGTGCCTCCTGGACAATCATTAGTGCGGGTAAGGCAGAGTATACATT
TTACGAGGGGATGGGCCCTGTCCTTGCCCCAGTCACACCGGTGCTTGTTGTAGAAAGTCTTCAGTTGAATGGCAGTGAGG
ATGTAGCAATCTTGAACTTCAGGACAGCATTTCACTCCAAATGTACGAGTGTGGTTTGGGGATGTAGAAGCTGAAACTAT
GTACAGATGTGGAGAGAGTATGCTCTGTATGCCCCAGACATTTCTGCATTCCGAGAAGATGGAGATGGGTCCGGCAGCCA
GTCCAGGTTCCAGTACTTTGGTCCGTAATGATGGATCATTTATTCACCAGCCTTACCTTTACCTACACC

Alignment

ORF - retro_ttru_1151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 85. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  KFGERPPPKRLTREAMRNYLKERGDQTVL-ILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKKK-EQME
          KFGE..PPK..TREAM..YLKE.GDQTVL.ILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWK.KK.EQME
Retrocopy KFGEWLPPK*FTREAM*SYLKEQGDQTVLLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKEKK<EQME

Parental  RDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDDIGVFLS
          RDGCSEQESQPCAFI.IGNSDQEMQQLN.EGKNYCTAKTLYISDSDKRKHFMLSVKMFYG.SDDIGVFLS
Retrocopy RDGCSEQESQPCAFIRIGNSDQEMQQLNWEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGSSDDIGVFLS

Parental  KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYIHLLDDD
          K.IKV.SKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTR.LHVEGGNFHASSQQW.AFYIHLLDDD
Retrocopy KQIKVTSKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRCLHVEGGNFHASSQQWAAFYIHLLDDD

Parental  ESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMY-
          ESEGEEFTV.DGYIHYGQTV.LVCSVTG.ALPRLIIRKVDKQTALLDA.DPVSQLHKCAFYLKDTERMY.
Retrocopy ESEGEEFTVHDGYIHYGQTVTLVCSVTGVALPRLIIRKVDKQTALLDAGDPVSQLHKCAFYLKDTERMY<

Parental  LCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGD
          LCLSQERI..FQATPCPKEPNKEMINDGASWTIIS..KAEYTFYEGMGPVLAPVTPV.VVESLQLNG..D
Retrocopy LCLSQERIVRFQATPCPKEPNKEMINDGASWTIISAGKAEYTFYEGMGPVLAPVTPVLVVESLQLNGSED

Parental  VAM-LEL-TGQNFTPNLRVWFGDVEAETMYRCGESMLCV-VPDISAFREG-WRWVRQPVQVPV-TLVRND
          VA..LEL..GQ.FTPN.RVWFGDVEAETMYRCGESMLC...PDISAFRE..WRWVRQPVQVPV.TLVRND
Retrocopy VAI<LEL<SGQHFTPNVRVWFGDVEAETMYRCGESMLCM<APDISAFRED<WRWVRQPVQVPV<TLVRND

Parental  G-IIYS-TSLTFTYT
          G.IIYS.TSLTFTYT
Retrocopy G<IIYS<TSLTFTYT

Legend:

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

Expression

RNA-Seq

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq

Tursiops truncatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ttru_1151 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1151 was not experimentally validated.

Homology

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151 , retro_ttru_1593,