RetrogeneDB ID: retro_ttru_1217

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_107418:261982..262852(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSTTRG00000013885
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_ttru_1217
AACACACATGAAGCAAGTAGATATCCAGTTCAAGACAAGATGCTACGCAAACCCACAGGATATACTGGATTAAGTGCAAA
AAGTTGTGCAGAAGCTGCTTTAGAGGAAGAAAGTTGACAGAGACAGTCTCGCATGGAGAAAGGAAAATCTTACATGAGCA
TTCAGCCTGCTGAAGATTCGATAATTACGATGATGGCTTTTCAATGAAGCAAACAGCTATAGCCCGTTTCCACAGAAACC
ACCGCCTCATCCGTGAAATCCTAAGTGAGAGTGTGGTGCCAGACGTTTGGTCAGTTGTCATAACAGCTAGAATGCAGGTC
CTCAAATGACAGGTCCAGTCCTTAATGGTTCATCAGTGAAAACTAGAAGCTGAACTTCTTCAAATAGAGGAGTGACACCA
AGAAAAGAAGAGGAAATTCCTGGAAAGCACAGATTCATTTAACAATGAACTTAAAAGCTTGTGTGGTTGAAAGTAGAAGT
GGATATGGAAAAATCTGCAGCTGAAATTGCACAGGCTGAGGAACAGGCTCACAAAAAGCAGGAAGAAAGGGAGAAAGAGG
CAGCAGCGCAAGCTGAGCACAGCCAGAGCAGTAGTGTTCCTGAGGAGGAGCCAGCAGCTAATAAGACCGAAGAAAAAAAG
ACAAGAGCGTCCTGAAGGACACAGAGGAGACACTCCTTGAAGAAACGACAGAAAGTCAACAGAATGGTAAAGAAGGCACA
TCTACTCCTGAGGACGAGGAGAGCGGGCAGGAGGGGGTGGACAGTCTGGCAGAGGAAGGGACCAGTGATAGTAACACGGG
CTTGGAGAGCAACAGCGCAACCGTGGAGGAGCCACCAACGGATCCCGTACCAGAAGATGGGAAAAAAGAA

Alignment

ORF - retro_ttru_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.26 %
• Parental protein coverage: 71.78 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDP-DDYDDG
          N..EA........M......P.......AKS.AEAALEEES.QRQSRMEKG..YMSIQPAED..D.YDDG
Retrocopy NTHEASRYPVQDKML---RKPTGYTGLSAKSCAEAALEEES*QRQSRMEKGKSYMSIQPAEDS<DNYDDG

Parental  FSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEK
          FSMK.TA.ARF.RNHRLI.EILSESVVPDV.SVV.TARMQVLK.QVQSLMVHQ.KLEAELLQIEE.HQEK
Retrocopy FSMKQTAIARFHRNHRLIREILSESVVPDVWSVVITARMQVLK*QVQSLMVHQ*KLEAELLQIEE*HQEK

Parental  KRKFLESTDSFNNELKRLCG-LKVEVDMEKIAAEIAQAEEQARKRQEEREKEAAEQAERSQSSIVPEEEP
          KRKFLESTDSFNNELK.LCG.LKVEVDMEK.AAEIAQAEEQA.K.QEEREKEAA.QAE.SQSS.VPEEEP
Retrocopy KRKFLESTDSFNNELKSLCG<LKVEVDMEKSAAEIAQAEEQAHKKQEEREKEAAAQAEHSQSSSVPEEEP

Parental  AANKTEEKKEDESIPMETEETH-LEETTESQQ-NGEEGTSTPEDKESGQEGVDSLAEEGTSDSNTGSESN
          AANKTEEKK...S....T...H.L.E.T...Q.NG.EGTSTPED.ESGQEGVDSLAEEGTSDSNTG.ESN
Retrocopy AANKTEEKKTRAS--*RTQRRH<LLEETTESQQNGKEGTSTPEDEESGQEGVDSLAEEGTSDSNTGLESN

Parental  SATVEEAPTDPVPEDGKKE
          SATVEE.PTDPVPEDGKKE
Retrocopy SATVEEPPTDPVPEDGKKE

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_1217 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1217 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016025	8 retrocopies	retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300, retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni	ENSCHOG00000008727	3 retrocopies	retro_chof_1245, retro_chof_482, retro_chof_573,
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus	ENSFCAG00000009646	2 retrocopies	retro_fcat_234, retro_fcat_513,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tursiops truncatus	ENSTTRG00000013885	1 retrocopy	retro_ttru_1217 ,