RetrogeneDB ID: retro_tbel_3816

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_16507:1523..2815(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC111
• Ensembl ID: ENSTBEG00000013589
• Aliases: None
• Description: coiled-coil domain containing 111 [Source:HGNC Symbol;Acc:26575]

Sequence

>retro_tbel_3816
ATGAAGAGGAAGTGGGAAGCAAAACTGAAACAAATTGAAGAGCGAGCACATCATTATGAGAGGAAACCACTGTTCTCCGT
GTATATACCACGGCTATGTAAGCCAGAAGAACCCCCCTCTGTTTGGAAACTCTTTCATCGGCAGACTGAAGCTTTTAATT
TTGTTAAAAGTTGTAAAGAGGACTTCAAGTATTTGCTTTGGAATACAAAGTGGGAGATGGACAACGTATTTACCTTGTAA
CAACTTATGTTTAGCTCTGGTTTTATTATAAATCCCAAAGAAACCTCTTGCACTGCTATGAAGTTATTCCTGAAAATGCT
GTGTGCAAGCTTTATTTTGATTTGGAATTTAACAAGCCGGCCAATCCAGGAGCCTATGGGAAAACAATGGTTGCATTACT
CGTTGAGCATGTTTGTAAAGCACTTCAAGAATTGTACAGTGTGACTTGTTCAGCCAAAGATGTTTTCAACATGGATTCTA
GCACTGATGAAAAATTTAGCCGCCATTTAATATTTCAGCTCCATGATGTGGTATTTAAAGATAACATTTATGTTGGTAAT
TTTGTGAAAAAAATTTTGCAGCCTGCTCTCCACTTAATTGCCAATGGAGAGAATGATTCAAGTCCAGGGACGACAGGACA
TAGATTTTCTCATTTTTCTGAAGCACCAATAAAACAAGGGATTTCCTCTAACAGAATGTCCACTGGTGAGGATATGGCAG
TGAGCTGGACACGGAGTTCAGAGAAACCAGAGAGGCCCAGGTCAGCGAGACCAAGCAGTCCTGATCTTTCCTTTTTGGTT
GTGAAGAATAACATGGGACAAAGGCATCTTTTTGTAGATCTAGGAGCTTATACAAGAAATAGAAACCTTTGGCTATATAA
ATCATCAAAAATAGGAGAATATGTGACTTTTGAGATCACTGAAGACAACAGATTTTTTCCTGTATAGTCAAAAAAGATTT
CTGAAGAAAATCAATATTTCCTCTATTCGTTGGTCACCAATATCAGATTCTCACATACTTTACGAATTCTTACATGTGAC
ACATCTCAGAATACAGAAGAGCAAGTTGAGCATTTTAATAGTTCCAGCACTTCAGTAAAAACCATTGAAGGTTTTCAGTG
TTCACCCTGCCCTGAAGTTGATCATTTTGTTCTTTCTTTGGTGAATAAAAATAATGTTAAAGGAGGGATTCGGCGCTGGA
ACTACTTTTTCCCAGAAGAATTATTGGTTTATGATATTTGTAGAAATCGCTGGTGGGAAAACATTGGAAGAGCCCACAAG
AGTAATAATATT

Alignment

ORF - retro_tbel_3816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 76.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKRKWEAKLKQIEERASRYERKPLFSVYRPRLCKPEEPPSIWKLFHRQTEAFNFVKSCKED-VHVFALEY
          MKRKWEAKLKQIEERA..YERKPLFSVY.PRLCKPEEPPS.WKLFHRQTEAFNFVKSCKED...VFALEY
Retrocopy MKRKWEAKLKQIEERAHHYERKPLFSVYIPRLCKPEEPPSVWKLFHRQTEAFNFVKSCKED<LQVFALEY

Parental  KVGDGQRIYLVTTYVQLWFYYKSRRNLLHCYEVIPENAVCKLYFDLEFNKPANPEADGKRMVALLIEHVC
          KVGDGQRIYLVTTYV.LWFYYKS.RNLLHCYEVIPENAVCKLYFDLEFNKPANP.A.GK.MVALL.EHVC
Retrocopy KVGDGQRIYLVTTYV*LWFYYKSQRNLLHCYEVIPENAVCKLYFDLEFNKPANPGAYGKTMVALLVEHVC

Parental  KALQELYGVTCSAKDVFNLDSSTDEKFSRHLIFQLHDVAFKDNIHVGNFVKKILQPALHFIASGEDDSGP
          KALQELY.VTCSAKDVFN.DSSTDEKFSRHLIFQLHDV.FKDNI.VGNFVKKILQPALH.IA.GE.DS.P
Retrocopy KALQELYSVTCSAKDVFNMDSSTDEKFSRHLIFQLHDVVFKDNIYVGNFVKKILQPALHLIANGENDSSP

Parental  ETTGHGFSRFSEAPVKQGISSNRMSTGEDTGASRTWSPEEPERPRSARPSSPDLSFLVVKNNTGEKRLFV
          .TTGH.FS.FSEAP.KQGISSNRMSTGED...S.T.S.E.PERPRSARPSSPDLSFLVVKNN.G...LFV
Retrocopy GTTGHRFSHFSEAPIKQGISSNRMSTGEDMAVSWTRSSEKPERPRSARPSSPDLSFLVVKNNMGQRHLFV

Parental  DLGVYTRNRNFRLYKSSKIGKRVAFEIAEDNKFFPEESNKVSEENQYFLYSLVTNIRFSDTLRILTCDTS
          DLG.YTRNRN..LYKSSKIG..V.FEI.EDN.FFP..S.K.SEENQYFLYSLVTNIRFS.TLRILTCDTS
Retrocopy DLGAYTRNRNLWLYKSSKIGEYVTFEITEDNRFFPV*SKKISEENQYFLYSLVTNIRFSHTLRILTCDTS

Parental  QHTEEQVERFNS---TVKTIEGFQCSPYPEVDHFVLSLVNKNDIKGGIRRWNYFFPEELLVYDICRYRWC
          Q.TEEQVE.FNS....VKTIEGFQCSP.PEVDHFVLSLVNKN..KGGIRRWNYFFPEELLVYDICR.RW.
Retrocopy QNTEEQVEHFNSSSTSVKTIEGFQCSPCPEVDHFVLSLVNKNNVKGGIRRWNYFFPEELLVYDICRNRWW

Parental  ENIGRAHKSNNI
          ENIGRAHKSNNI
Retrocopy ENIGRAHKSNNI

Legend:

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

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3816 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3816 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tupaia belangeri	ENSTBEG00000013589	1 retrocopy	retro_tbel_3816 ,