RetrogeneDB ID: retro_ttru_1038

Retrocopy location

• Organism: Dolphin (Tursiops truncatus)
• Coordinates: scaffold_100600:39357..40889(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCD1
• Ensembl ID: ENSTTRG00000001010
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 [Source:HGNC Symbol;Acc:11106]

Sequence

>retro_ttru_1038
ATGGTGGCCCGGGCGGCTTTCCAGTCTGTGGCTCCGAGCGGCGGCGCTGGAGCCTCAGGAGGGGCGGGCGCGGCGGCTGC
CCTGGGTCTGGGCGGGCCTCCGGGGCCTCCGGTGCGAATGGGCCCGGCGCCGGGTCAAGGGCTGTACCGCTCCCCGATGC
CCGGAGCGGCCTATCCGAGACCAGGTATGCTACCAGGCAGCCGAATGACACCTCAGGGACCTTCCATGGGACCCCCTGGC
TATGGGGGGAAACCTTCAGTCCTACCTGGCCTGGCCCAGTCAGGGATGGACCAGTCCCTCAAGAGACCTGCACCTCAGCA
GGTCCAGCAGCAGCAGTCCAAAATCGGAACCACAATGCAAAGAAAAAGAAGATGACTGACAAAATTCTACCTCAAAGGAT
TCGTGAACTGTACCAGAATCCCAGGCCTATATGGATCTCTTGGCTTTTGAAGGAAACTGGACCAGACTATCATGAGAAAC
AGCTAGATATGCAGGAAGCCTTGGAACGTCCCATCAAGAAAAAACGGAAGCTGCGAATTTTCATTTCTAACACTTTCAAT
CCGGCTAAGTCAGATGCTGAGGATGGGGAAGGGACGGTGGCTTCCTGGGAGCTTCGGGTAGAAGGACGGCTCCTGGAGGA
TTCAGCCTTGTCCAAATATGATGCCACCAAACAAAAGAGGAAGTTCTCTTCTTTTTTTAAGTCCTTGGTGATCGAACTGG
ACAAAGACCTGTATGGGCCAGATAACCATCTGGTGGAATGGCACAGGACCGCCACTACCCAGGAGACAGATGGCTTCCAG
GTGAAGCGGCCAGGATGTGTGAATGTACGGTGTACTGTCCTGCTGATGCTGGATTACCAGCCTCCTCAGTTTAAATTAGA
CCCTCGTCTGGCTCTGCTGCTGGGCATCCACACCCAGACCCGTCCAGTGATCATTCAAGCACTGTGGCAATATATTAAGA
TGCATAAGCTCCAGGACCCACATGAGCAGGAGTTTGTTATCTGTGACAAGTACCTCCAGCAGATCTTTGAGTCTCAACCT
ATGACGTTTTCAGAGATCCCCCAACAGCTCCACGCCTTGCTTATGCCACCAGAGCCCATCATCATTAATCATGTCATCAG
TGTTGACCCGAATGATCAGAAAAAGACAGCGTGTTATGACATCGATGTGGAAGTGGATGATACCTTGAAGACCCAGATGA
ATTCTTTTCTGCTGTCTACTGCCAGCCAGCAGGAGATTGCTACTCTAGACAACAAGATCCATGAGACAATAGAAACTATC
AATCAGCTGAAGACCCAGCAAGAGTTCATGCTGAGCTTTGCCAGAGACCCTCAGGGTTTCATCAATGACTGGCTTCAGTC
CCAGTGCTGGGACCTCAAGACCATGACTGATGTGATGGGTAACCCAGAAGAAGAGCGCCGAGCTGAGTTCTACTTCCAGC
CTTGGGCACAGGAGGCCGTGTGCCGATGCTTCTGCTCCAAGATGCAGCAGAGACGACAAGAATTAGATCAAGCCCTGGGA
ATCCGAAACACA

Alignment

ORF - retro_ttru_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.45 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAARAGFQSVAPSGGTGASGGAGAAAALGPGGTPGPPVRMGPAPGQGLYRSPMPGAAYPRPGMLPGSRMT
          M.ARA.FQSVAPSGG.GASGGAGAAAALG.GG.PGPPVRMGPAPGQGLYRSPMPGAAYPRPGMLPGSRMT
Retrocopy MVARAAFQSVAPSGGAGASGGAGAAAALGLGGPPGPPVRMGPAPGQGLYRSPMPGAAYPRPGMLPGSRMT

Parental  PQGPSMGPPGYGGNPSVRPGLAQSGMDQSRKRPAPQQIQQVQQQ-AVQNRNHNAKKKKMADKILPQRIRE
          PQGPSMGPPGYGG.PSV.PGLAQSGMDQS.KRPAP...QQVQQQ.AVQNRNHNAKKKKM.DKILPQRIRE
Retrocopy PQGPSMGPPGYGGKPSVLPGLAQSGMDQSLKRPAP---QQVQQQ<AVQNRNHNAKKKKMTDKILPQRIRE

Parental  L-VPESQAYMDLLAFE-RKLDQTIMR-KRLDIQEALKRPIKQKRKLRIFISNTFNPAKSDAEDGEGTVAS
          L.VPESQAYMDLLAFE.RKLDQTIMR.K.LD.QEAL.RPIK.KRKLRIFISNTFNPAKSDAEDGEGTVAS
Retrocopy L<VPESQAYMDLLAFE<RKLDQTIMR<KQLDMQEALERPIKKKRKLRIFISNTFNPAKSDAEDGEGTVAS

Parental  WELRVEGRLLEDSALSKYDATKQKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTATTQETDGFQVKRPG
          WELRVEGRLLEDSALSKYDATKQKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTATTQETDGFQVKRPG
Retrocopy WELRVEGRLLEDSALSKYDATKQKRKFSSFFKSLVIELDKDLYGPDNHLVEWHRTATTQETDGFQVKRPG

Parental  DVNVRCTVLLMLDYQPPQFKLDPRLARLLGIHTQTRPVIIQALWQYIKTHKLQDPHEREFVICDKYLQQI
          .VNVRCTVLLMLDYQPPQFKLDPRLA.LLGIHTQTRPVIIQALWQYIK.HKLQDPHE.EFVICDKYLQQI
Retrocopy CVNVRCTVLLMLDYQPPQFKLDPRLALLLGIHTQTRPVIIQALWQYIKMHKLQDPHEQEFVICDKYLQQI

Parental  FESQRMKFSEIPQRLHALLMPPEPIIINHVISVDPNDQKKTACYDIDVEVDDTLKTQMNSFLLSTASQQE
          FESQ.M.FSEIPQ.LHALLMPPEPIIINHVISVDPNDQKKTACYDIDVEVDDTLKTQMNSFLLSTASQQE
Retrocopy FESQPMTFSEIPQQLHALLMPPEPIIINHVISVDPNDQKKTACYDIDVEVDDTLKTQMNSFLLSTASQQE

Parental  IATLDNKIHETIETINQLKTQREFMLSFARDPQGFINDWLQSQCRDLKTMTDVVGNPEEERRAEFYFQPW
          IATLDNKIHETIETINQLKTQ.EFMLSFARDPQGFINDWLQSQC.DLKTMTDV.GNPEEERRAEFYFQPW
Retrocopy IATLDNKIHETIETINQLKTQQEFMLSFARDPQGFINDWLQSQCWDLKTMTDVMGNPEEERRAEFYFQPW

Parental  AQEAVCRYFYSKVQQRRQELEQALGIRNT
          AQEAVCR.F.SK.QQRRQEL.QALGIRNT
Retrocopy AQEAVCRCFCSKMQQRRQELDQALGIRNT

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_1038 retrocopy.

TSS

Tursiops truncatus was not studied using FANTOM5 data.

Lab

retro_ttru_1038 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000037935	1 retrocopy	retro_btau_1829,
Tursiops truncatus	ENSTTRG00000001010	2 retrocopies	retro_ttru_1022, retro_ttru_1038 ,
Tursiops truncatus	ENSTTRG00000006988	1 retrocopy	retro_ttru_1394,